ABC transporter: ATP-binding cassette transporter. It is important for transporting bacteriocines out of bacterial cells. Transporters in the same class also play an important role in AMP sensing and/or detoxification.

Abu-S-Ala: methyl lanthionines (cf. Ala-S-Ala, lanthionines)

AD: Atopic Dermatitis or /Eczema (AE), a diseased condition where expression of AMPs such as hCAP-18/LL-37 is suppressed.

ADME: the processes of a compound is Absorbed, Distributed, Metabolized, and Excreted from the human body (or an organism such as mice, dog, and monkeys).

Aerosols: particles less than 5 um

AFM: Atomic Force Microscopy

AI: artificial intelligence. Since the success of protein structure prediction by AlphaFold, AI is getting hot every day. 99% of AI is based on deep learning.

AIM2: Absent in melanoma 2, recognize cytosolic dsDNA

Alarmins: structurally distinct peptide mediators that can recruit and activate antigen-presenting cells (APCs), thereby enhancing immune response. See also DAMP.

AlphaFold 2: a state of the art protein structure prediction tool (2021 Nature) based on AI and structural data in the PDB. Database for predicted structures for over 200 million proteins

Amino acid : A, Ala, alanine; C, Cys, cysteine; D, Asp, asparate; E, Glu, glutamate; F, Phe, phenylallanine; G, Gly, glycine; H, His, histidine; I, Ile, isoleucine; K, Lys,lysine; L, Leu, leucine; M, Met, methionine; N, Asn, asparagine; P, Pro, proline; Q, Gln, glutamine; R, Arg, arginine; S, Ser, serine; T, Thr, threonine; V, Val, valine; W, Trp, tryptophan; and Y, Tyr, tyrosine. SEE ALSO Non-standard AA below.

Amino acid rich peptides: Traditionally, rich antimicorbial peptides refer to those that form neither alpha nor beta structures. However, "Rich" can be used as an independent criterium for peptide classification. Approximately 21% antimicrobial peptides are rich in certain amino acid in the antimicrobial peptide database.

ALT: (serum) alanine aminotransferase, a standard biomarker for liver damage

AMPs : antimicrobial peptides. See also HDP and innate immune peptides

AKT: v-akt murine thymoma viral oncogene homolog 1

ALR: AIM2-like receptor, recognize dsDNA viruses, one of the 5 families of the pattern-recognition receptors (TLR, CLR, NLR, RLR, ALR)

AP-1: Activated Protein-1, a transcription factor

APC: Antigen Presenting Cell

APD : The Antimicrobial Peptide Database, or the AMP database.

API: Active Pharmaceutical Ingredient

Archaeocins : Proteinaceous antimicrobials from the domain archaea

ATAC-Seq: Assay for Transposase-accessible chromatin with sequencing

ATCC: American Type Culture Collection, founded in 1925, is a repository for donated bacterial strains.

Bacteriocins: Proteinaceous antimicrobials from the domain bacteria. For Gram-positive bacteria, class I bacteriocins are lantibiotics whose polypeptide chains are subject to extensive chemical modifications after translation. Type A has an elongated structure while type B has a more rigid and globular structure. Class II bacteriocins possess unmodified polypeptide chains. This class is further divided into class IIa (the pediocin-like bacteriocins), class IIb (the two-peptide chain bacteriocins, class IIc (cyclic peptides), and class IId (the leaderless peptide bacteriocins). Classes III are large proteins with lytic activity (Cotter P et al., 2005 Nature Rev Microbiol 3: 777). Bacteriocins from Gram-negative bacteria are called microcins (Class I < 5 kDa; Class II, 5-10 kDa; and class III(colicins) > 10 kDa (Duquesne et al. 2007 Nat. Prod. Rep. 24: 708-734).

BB codes for peptide binding partners : BBB, peptide self association; BBII, metal ions; BBL, LPS; BBMm, membranes; BBN, nucleic acids; BBPP, protein/enzyme; BBS, sugars. AMPs with such activities can be searched in the name field of the search interface of the APD by entering the code.

BCAA : Branched chain amino acids;

BGCs : biosynthetic gene clusters;

Black death: a plague caused by the deadly bacterium Yersinia pestis.

BLAST: Basic Local Alignment Search Tool

BLP: Bacterial LipoProtein, TLR2/1 ligand (recognizing Gram+ bacterial cell wall). This BLP binding to TLR2/1 upregulates the expression of vitamin D receptor and the vitamin D-1-hydroxylase genes, leading to the induction of human cathelicidin LL-37 to kill Mycobacterium tuberculosis.

Boman Index : Originally called protein-binding potential by Hans Boman. It was renamed as Boman Index when it was introduced into the APD in 2003. Boman index is the sum of the free energies of the respective side chains for transfer from cyclohexane to water taken from Radzeka and Wolfenden and divided by the total number of the residues of an antimicrobial peptide. The calculated values are negative ( except for the hybrid peptide), but the + and - are reversed. A more hydrophobic peptide tends to have a negative index, while a more hydrophilic peptide tends to have a more positive index [Boman, H.G.(2003) J.Inter.Med.254:197-215].

CAPA: Corrective Action, Preventative Action (FDA)

CARD: caspase recruitment domain

Cathelicidin: a family of antimicrobial peptides that share the common N-terminal cathelin domain in their precursor proteins

CPP: cell-penetrating peptides can enter eukaryotic cells. "Cell-penetrating" is searchable in the Name field of the APD.

CD: Circular Dichroism, especially good at estimating helix formation with the change in conditions.

CDC: US Centers for Disease Control and Prevention

CEM cells: a human CD4+ T-cell line. It has been used to screen for anti-HIV peptides.

CF: Cystic Fibrosis

CFPS: cell-free protein/peptide synthesis. The use of this system can overcome the toxicity to the expression host (PubMed 1980).

CFU: Colony-Forming Unit

cGAS: Cyclic GMP-AMP synthase.

Chagas disease: Chagas found Trypanosoma cruzi is the causing agent of the disease.

Chemokines : separated into four subfamilies based on the distinctive pattern of the two N-terminal cysteines: CXC (alpha), CC (beta), C and CX3C classes (nomenclature)

ChIKV: Chikungunya virus, a positive-sense, single-stranded RNA virus in the Alphavirus genus. Infected via mosquitoes.

ChIP: Chromatin ImmunoPrecipitation assays

Citrullination: a process (also called deimination) where the peptidyl arginine residue is converted to citrulline by an enzyme (peptidyl arginine deiminase, PAD). Citrullination is a normal reaction during cell death. It also occurs at sites of inflammation. Human LL-37 could be modified in this manner.

CLR: C-type lectin receptor, one of the 5 families of the pattern-recognition receptors (TLR, CLR, NLR, RLR, ALR)

CMC: Critical Micelle Concentration

CNN: Convolutional Neural Network, a common deep learning artchitecture

CNS: Central nervous System

Colicins : see microcins.

Collectins: Collagenous lectins, which could bind to viruses and thereby protect the host.

COPD: chronic obstructive pulmonary disease, where host defense peptides such as LL-37 may play a role.

Core peptide: in the lantipeptide case, it refers to the C-terminal region of the precursor that becomes the final AMP after processing . In other cases, it is also used to refer to the critical AMP region that retains antimicrobial activity (e.g., Li et al. 2016).

CoVID-19: Coronavirus disease 2019

CpG-ODN: CpG-OligoDeoxyNucleotides (DNA), unmethylated, TLR9 ligand

CQAs: Critical Qaulity Attributes such as viscosity, pH, density, or content uniformity

CRE: Carbapenem-resistant Enterobacteriaceae, the "Nightmare bacteria" (CDC director Tom Frieden) detected in over 200 USA hospitals in 2012. Go to the CDC website

Crohn's disease: a chronic inflammatory bowel disease due to a defect in intestinal innate immune responses to bacteria

CryoEM: Cryogenic electron microscopy

cSSTIs: complicated skin and soft tissue infections (e.g. by Staph)

CT: Computed Tomography

CTD: Common Technical Document

Cyclotides: Plant circular peptides that have no exposed N- or C-terminal residues (listed here).

25D: 25-hydroxyvitamin D3, the major circulating form. Once converted to 1,25D, it can induce LL-37 expression in human cells.

1,25D: 1,25-dihydroxylvitamin D3, the active form of vitamin D that induces the expression of LL-37, hBD-2, and intracellular pattern recognition receptor called NOD2/CARD15 in humans.

D8PG: Dioctanoylphosphatidylglycerol, a bacterial membrane-mimicking model for structural studies of membrane-bound peptides such as AMPs. Refer to SDS.

DAMP: damage-associated molecular patterns. Examples are alarmins (defensins, cathelicidins, high-mobility group box-1 protein (HMGB1), and iron-binding proteins) and mitochondrial DNA of eukaryotic cells.

Deamination: see Citrullination

Dectin: Dendritic Cell-associated C-type lectin

DENV: Dengue virus

Dha: 2,3-didehydroalanine, dehydrated serine (Ser), or occasionally Cys (Claesen and Bibb 2010 PNAS 107:16297)

Dhb: (Z)-2,3-didehydrobutyrine, dehydrated threonine (Thr)

DMPC: 1,2-dimyristoyl-sn-glycero-3-phosphocholine, a 14-carbon zwitterionic lipid used to mimic phopholipids.

DMPG: 1,2-Dimyristoyl-sn-glycero-3-phosphoglycerol, a 14-carbon anionic lipid used to mimic phopholipids.

DoD: Department of Defense, USA

DOI: Digital Object Identifier, aunique number to cite an accepted and in press manuscript before the print publication.

DPC: Dodecylphosphocholine, a synthetic detergent used to mimic membranes (e.g., human cells) for structural studies by CD or NMR.

dpi: (immunology) days post-infection

droplet: particles greater than 5 um

Drug compounding: a little-known practice in which pharmacists traditionally alter or recombine drugs to meet the special needs of specific patients, e.g. HIV-1 cocktail therapy

DSC: Differential Scanning Calorimetry

DSSP: Database of secondary structure assigments. It calcualtes secondary structures for proteins/peptides in the PDB but does not do prediction. Visit the APD website "3D structure of AMPs" for information on structural determination of AMPs to high quality.

EboV: Ebola Virus

ectodomain: the extracellular domain of a membrane protein, usually for recognition followed by signal transduction.

eDNA: extracellullar DNA, i.e. genomic DNA released by bacteria, an important component involved in the formation of bacterial biofilms.

EEE: Eastern equine encephalitis, Triple E or sleeping sickness

EGFR: Epidermal Growth Factor Receptor

ELISA: Enzyme-linked immunosorbent assay

ENCODE: The Encyclopedia of DNA Elements, a public research resource that contains a comprehensive parts list of functional elements in the human genome

EST: Expressed Sequence Tag

ER: Endoplasmic Reticulum

ESBL: extended-spectrum ß-lactamase

ESKAPE pathogens: the abbreviation of the six multi-drug resistant bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species.

EUA : an emergency use authorization such as saliva test or vaccines for COVID-19

Eucaryocins : Proteinaceous antimicrobials from the domain eucarya

FACS: Fluorescence-Activated Cell Sorter

FASTA: A universal bioinformatic text-sharing format that begins with a comment followed by single-lettered amino acids or nucleotides.

FDA: US Food and Drug Administration

Firmicutes: the low-G+C-content gram-positive bacterial species, e.g. bacilli & clostridia.

FICI: fractional inhibition concentration index, a number used to gauge synergistic interactions of molecules (FICI < 0.5 synergy; FICI >1, antagonism).

FITC: Fluorescein isothiocyanate, a flurescent probe widely used in tracing the location of antimicrobial peptides in cells. Peptides that can enter eukaryotic cells are called "cell-penetrating peptides".

FPRL1: Formyl Peptide Receptor-Like 1. Human Ll-37 chemoattracts human neutrophils, monocytes, T cells and multipotent mesenchymal stromal cells (stem cells) by binding to this cell surface receptor. This molecular process could be essential for cancer metastasis (see the minireview on the relationship between LL-37 and cancer, Wu W.K.K. et al. 2010 Int J cancer 127:1741-7).

FRET: Fluorescence Resonance Energy Transfer

FT-IR: Fourier Transform InfraRed spectroscopy

GCP: Good Clinical Practice (FDA). See also GLP and GMP.

GI: gastrointestinal

GLP: Good Laboratory Practice (FDA) . See also GCP and GMP.

Glycopeptides: glycolated peptides with antimicrobial activity (newly discovered from bacteria in 2011). These are regarded as examples for the class IV peptide (conjugated peptides) originally proposed by Klaenhammer (1993).

GM-CSF: Granulocyte�Macrophage Colony-Stimulating Factor

GMP: Good Manufacturing Practice (FDA)

GO: Gene Ontology (for instance)

GRAS: Generally Recognized As Safe

GRAVY: Grand average of hydropathicity index. Proteins with a positive GRAVY are more hydrophobic and thereby less soluble, while proteins with a negative GRAVY value are more hydrophilic and tend to be more water soluble (Kyle and Doolittle, 1982).

GWAS: Genomewide association studies

hBD: human Beta Defensin (28 genes in humans, most well studied are HBD-1, HBD-2, HBD-3, and HBD-4)

hCAP-18: human Cationic Antimicrobial Protein of 18 kDa (i.e., the precursor of human cathelicidins LL-37 and ALL-38, the mature antimicrobial peptides; originally thought FALL-39). The gene that encodes this protein is referred to as CAMP.

HD5: see "HNP"

HD6: see "HNP"

HDP: see "Host Defense Peptide"

HIV-1: Human immunodeficiency Virus type 1

HNP: Human Neutrophil Protein, HNP-1 to HNP-4 made in granulocytes, and human defensins 5 and 6 (HD-5 and HD-6) made in Paneth cells. All these are human alpha defensins.

Host Defense Peptide: An alternative name for antimicrobial peptides that emphasizes the immune modulation activities of AMPs.When needed, a more general term innate immune peptides may also be utilized (See the APD main page).

HPLC: High-performance liquid chromatography, important for peptide purification

hRBC: Human red blood cells (erythrocytes), frequently used for toxicity test of AMPs.

HSP: Heat Shock Proteins, identified binding targets for Pro-rich AMPs. However, the molecular target could be ribosomes based on recent results (Krizsan A. et al., 2014).

HSV: Herpes Simplex Virus.

IACUC: Institutional Animal Care and Use Committee. It is a must that you get an approval prior to your testing of the efficacy of your favorite AMP candidates.

IAPs: Inhibitors of apoptosis proteins.

IAV: Influenza A Virus that causes seasonal Flu.

IBC: Institutional Biosafety Committee.

IBD: Inflammatory bowel disease

IC50: the concentration that inhibits 50% of the activity

ICK: inhibitor cystine knot found in most spider venom toxins.However, venom peptides with antimicrobial activity appear to be exceptions to this.

IDR: Innate Defence Regulator, which may not kill bacteria directly.

IFN-gamma: interferon-gamma

Ig: immunoglobulin

IHC: Immunohistochemistry

IkB: Inhibitor of NF-kB

IKK: Inhibitor of Kappa light polypeptide gene enhancer in B-cells, signaling molecules

IL: InterLeukin

IM: intramuscular (injection)

Imd: another major pathway in Drosophila that regulates the expression of antimicrobial peptides. The imd pathway is induced primarily by Gram-negative bacteria, while the Toll pathway is induced by Gram-positive bacteria and fungi. Disruption of toll caused clear fungal infection of the insect.

IND: Investigational New Drug (FDA)

Innate immune peptides: a more general term for the antimicrobial peptide field. It basically covers all the functions of such peptides known or to be discovered (Wang G ed. 2017 Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies, CABI). See also AMPs or HDP.

iNOS: inducible Nitric Oxide Synthase

Instability index: This index provides an estimation of peptide stability. It was developed based on the occurance of certain dipeptides in the sequence and reflects in vivo half life of the peptide (Guruprasad K et al., 1990).

IP: intraperitoneal (injection)

iPSC: induced pluripotent stem cells

IPTG: IsoPropyl beta-D-1-ThiogalactoPyranoside, a compound frequently used to induce antimicrobial peptide expression in E. coli. Recombinant expression systems are annotated in the APD since 2023.

IRAK: Interleukin-1 Receptor Associated Kinase

IRB: Institutional Review Board. A key goal of IRB is to protect human subjects from harm physically, emotionally, or psychologically.

IRF3: Interferon Regulatory Factor 3, a transcription factor (activated by phosphorylation)

ITAM: immunoreceptor tyrosine-based activation motif

JAK-STAT: Janus family tyrosine kinase-signal transduction and activators of transcription

ITC: Isothermal Titration Calorimetry

IV: intravenous (injection)

JEV: Japanese Encephalitis Virus that causes brain infection, which spreads via mosquitoes. Pigs and wild birds contain such a virus.

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kinocidins: Chemokines with antimicrobial activity. On the other side of the coin, some antimicrobial peptides such as human LL-37 and HBD-3 are now demonstrated to have chemotactic activity. Search the APD for more.

KPC: Klebsiella pneumoniae carbapenemase

LAB: Lactic Acid Bacteria that produce lantibiotics useful for food preservation.

LAM: LipoArabinoMannan, a glycolipid associated with the cell wall of Mycobacterium tubercolosis

Lan: meso-lanthionine

LanA: the peptide precursor to be processed by lantipeptide modification enzymes

Lantibiotics: lanthionine containing antibiotics which are extensively modified post-translationally.

Lantipeptides: lanthionine containing natural peptides with or without antimicrobial activity.

LBP: LPS-Binding Protein, its complex with LPS binds to CD14 high-affinity LPS receptor on the cell surface and induces cellular response via TLR4, the first mammalian homolog of Drosophila Toll. AMPs such as human LL-37 could compete with LBP, thereby suppressing, at least partially, the lethal effect of LPS-induced immune reponses. The synergistic binding of LPS to human LL-37 may be understood from the two hydrophobic domains due to the existence of Ser9 on the hydrophobic surface of the long amphipathic helix (Wang et al. 2012 Biochemistry 51:653-664). Abstract.

LC50: (50%) Median Lethal Concentration

LC-MS: Liquid Chromatography-Mass Spectrometry

Leader peptide: in the case of lantibiotics, it refers to the N-terminal region of the precursor important for production but unmodified and removed after processing

Lipids: PC, diacyl phosphatidylcholines; PG, diacyl phosphatidylglycerols; PE, diacyl phosphatidylethanolamine